Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "cd4"
graph_weight
## [1] "2.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   16.00   20.00   20.00   20.18   21.00   22.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 16 18 19 19 19 19 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
## [26] 20 21 21 21 21 21 21 21 21 21 22 22 22 22 22

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"   
## [1] "MARS"
## [1] "MARS1" "SLA2" 
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1951    49
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    45  1906    49
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##      sym_in_data   sym_limma
##  1:      ADPRHL2       ADPRS
##  2:          AES        TLE5
##  3:     C12orf45    NOPCHAP1
##  4:      C3orf58      DIPK2A
##  5:      C6orf99   LINC02901
##  6:        CBWD2       ZNG1B
##  7:      CXorf57        RADX
##  8:      FAM102A       EEIG1
##  9:      FAM122C      PABIR3
## 10:      FAM153C    FAM153CP
## 11:     FAM160A2      FHIP1B
## 12:        GRASP     TAMALIN
## 13:        H2AFX        H2AX
## 14:    HIST1H2AG      H2AC11
## 15:    HIST1H2BC       H2BC5
## 16:    HIST1H2BK      H2BC12
## 17:    HIST1H2BN      H2BC15
## 18:     HIST1H3A        H3C1
## 19:     HIST1H3H       H3C10
## 20:     HIST1H4C        H4C3
## 21:    HIST2H2BF      H2BC18
## 22:         LRMP       IRAG2
## 23:      MFSD14C    MFSD14CP
## 24:         MKL1       MRTFA
## 25:         MPP6    MPHOSPH6
## 26:  RNASEH1-AS1  RNASEH1-DT
## 27:        SEPT6     SEPTIN6
## 28:        SEPT9     SEPTIN9
## 29: TMEM161B-AS1 TMEM161B-DT
## 30:        ARNTL       BMAL1
## 31:     C6orf106       ILRUN
## 32:     C6orf203      MTRES1
## 33:      FAM129A      NIBAN1
## 34:     FAM160B1      FHIP2A
## 35:      FAM192A    PSME3IP1
## 36:        HEXDC        HEXD
## 37:     HIST1H1E        H1-4
## 38:     KIAA0100       BLTP2
## 39:     KIAA1551       RESF1
## 40:         LARS       LARS1
## 41:         MARS       MARS1
## 42:      PLA2G16      PLAAT3
## 43:        SEPT2     SEPTIN6
## 44:       SMIM37        MTLN
## 45:         YARS       YARS1
##      sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 2000    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:       ABCD3     ABCD3       ABCD3
## 2:       ABCG1     ABCG1       ABCG1
## 3:       ABHD5     ABHD5       ABHD5
## 4:        ABI1      ABI1        ABI1
## 5:      ABLIM1    ABLIM1      ABLIM1
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1    2 
## 1998    1
gene_info[gene_symbol %in% names(t1)[t1 == 2],]
##    sym_in_data sym_limma gene_symbol
## 1:       SEPT6   SEPTIN6     SEPTIN6
## 2:       SEPT2   SEPTIN6     SEPTIN6
gene_info[sym_in_data == "HIST1H2BC", gene_symbol:="H2BC4"]
gene_info[sym_in_data == "HIST1H2BG", gene_symbol:="H2BC8"]
gene_info[sym_in_data == "SEPT6", gene_symbol:="SEPTIN6"]
gene_info[sym_in_data == "SEPT2", gene_symbol:="SEPTIN2"]

Read in cell type-specific expression data

Cell type specific gene expression were downloaded from protein atlas.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)
## [1] 1587110       4
ct[1:5,]
##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5
length(unique(ct$`Cell type`))
## [1] 79
table(ct$`Cell type`)
## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090
ct_immune = fread("../Annotation/rna_immune_cell_monaco.tsv.gz")
dim(ct_immune)
## [1] 602700      5
ct_immune[1:5,]
##               Gene Gene name                Immune cell TPM pTPM
## 1: ENSG00000000003    TSPAN6                   basophil  NA  1.2
## 2: ENSG00000000003    TSPAN6  Central memory CD8 T-cell  NA  1.7
## 3: ENSG00000000003    TSPAN6         classical monocyte  NA  0.2
## 4: ENSG00000000003    TSPAN6 Effector memory CD8 T-cell  NA  0.7
## 5: ENSG00000000003    TSPAN6    Exhausted memory B-cell  NA  0.7
summary(ct_immune$TPM)
##    Mode    NA's 
## logical  602700
summary(ct_immune$pTPM)
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
##     0.00     0.00     3.10    49.74    27.20 96572.50
summary(ct_immune$pTPM[ct_immune$pTPM > 0])
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
##     0.10     1.70    11.60    67.96    42.80 96572.50
length(unique(ct_immune$`Immune cell`))
## [1] 30
table(ct_immune$`Immune cell`)
## 
##                            basophil           Central memory CD8 T-cell 
##                               20090                               20090 
##                  classical monocyte          Effector memory CD8 T-cell 
##                               20090                               20090 
##             Exhausted memory B-cell               intermediate monocyte 
##                               20090                               20090 
##                         MAIT T-cell               Memory CD4 T-cell TFH 
##                               20090                               20090 
##               Memory CD4 T-cell Th1          Memory CD4 T-cell Th1/Th17 
##                               20090                               20090 
##              Memory CD4 T-cell Th17               Memory CD4 T-cell Th2 
##                               20090                               20090 
##                          myeloid DC                        naive B-cell 
##                               20090                               20090 
##                    naive CD4 T-cell                    naive CD8 T-cell 
##                               20090                               20090 
##                          neutrophil                             NK-cell 
##                               20090                               20090 
##              non-classical monocyte          Non-switched memory B-cell 
##                               20090                               20090 
##                       Non-Vd2 gdTCR                         Plasmablast 
##                               20090                               20090 
##                     plasmacytoid DC                     Progenitor cell 
##                               20090                               20090 
##              Switched memory B-cell                               T-reg 
##                               20090                               20090 
## Terminal effector memory CD4 T-cell Terminal effector memory CD8 T-cell 
##                               20090                               20090 
##                          total PBMC                           Vd2 gdTCR 
##                               20090                               20090
lineage = fread("../Annotation/rna_immune_cell_monaco_cell_types.tsv")
dim(lineage)
## [1] 30  2
lineage[1:2,]
##     Cell_type      Lineage
## 1:   Basophil Granulocytes
## 2: Neutrophil Granulocytes

Check gene expression for each gene set

dim(gene_info)
## [1] 2000    3
for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct_immune$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct_immune[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Immune cell`) %in% 
                  str_to_lower(lineage$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Immune cell`), 
               str_to_lower(lineage$Cell_type))
  
  df = cbind(df, lineage[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = lineage$Cell_type)
  df = df[df$Lineage != "Total PBMC",]
  df$Lineage   = factor(df$Lineage, 
                        levels = setdiff(lineage$Lineage, "Total PBMC"))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(pTPM + 0.1), fill=Lineage)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}
## [1] 1
##  [1] "CHD2"     "ENOSF1"   "GRASP"    "JPX"      "PHYH"     "TBCCD1"  
##  [7] "TCTA"     "YPEL2"    "ZNF831"   "ABHD2"    "ERICH1"   "GNPAT"   
## [13] "IRAK4"    "MORC3"    "NLRC5"    "ODF3B"    "PEX11B"   "SEC14L1" 
## [19] "TNFRSF18" "ZBP1"     "ZNF236"  
## [1] "found 20 genes."

## [1] 2
##  [1] "ARHGAP9"  "ARID4A"   "CCM2"     "CD96"     "CITED2"   "DGKA"    
##  [7] "HELQ"     "HIST1H3H" "IFRD1"    "ING2"     "MXD1"     "RCAN3"   
## [13] "RGCC"     "RIC1"     "SLC12A7"  "SLC8B1"   "STARD10"  "TESPA1"  
## [19] "TMEM204"  "WARS2"   
## [1] "found 20 genes."

## [1] 3
##  [1] "AC093323.1"  "AC245297.3"  "ERVK3-1"     "FAM122C"     "GPCPD1"     
##  [6] "LINC01215"   "LINC02265"   "MAP3K2"      "MDS2"        "PLCL1"      
## [11] "SLC25A32"    "ST7L"        "TBPL1"       "TRAV38-2DV8" "TRBV5-4"    
## [16] "TRBV6-6"     "TRBV7-3"     "TTC3"        "ZNF506"      "MIR4435-2HG"
## [21] "PMVK"       
## [1] "found 15 genes."

## [1] 4
##  [1] "AC007952.4" "AC025164.1" "AC087239.1" "ATP2B1-AS1" "CD82"      
##  [6] "CSKMT"      "IER2"       "ILF3-DT"    "LBH"        "LINC00861" 
## [11] "NPIPB4"     "NUP58"      "PPP1R15A"   "PRR7"       "SLC2A3"    
## [16] "TAGAP"      "WHAMM"      "Z93241.1"   "AZI2"       "CCDC43"    
## [21] "ITGAL"      "N4BP1"     
## [1] "found 15 genes."

## [1] 5
##  [1] "CCDC66"    "CDC42SE2"  "CEP95"     "EPHB6"     "FHIT"      "FOXN3"    
##  [7] "HIST1H2BC" "NR4A3"     "NSUN6"     "PIK3IP1"   "PLK3"      "RSRP1"    
## [13] "SENP7"     "SLC44A1"   "WSB1"      "ZFP36L1"   "ITK"       "RECK"     
## [19] "SAMD9"    
## [1] "found 19 genes."

## [1] 6
##  [1] "ABHD5"      "AC119396.1" "AC245014.3" "AL133415.1" "AL139246.5"
##  [6] "ARL4A"      "ATG9B"      "FBXO3"      "IL23A"      "LTB"       
## [11] "MCUB"       "MHENCR"     "NAA16"      "NOP53"      "POLD4"     
## [16] "SCML4"      "SLC25A38"   "SNRK"       "TBCC"       "TNFRSF25"  
## [21] "ZC3H12D"   
## [1] "found 16 genes."

## [1] 7
##  [1] "COQ7"    "IER3"    "MZF1"    "ADGRE5"  "ARL4C"   "C1orf21" "CFD"    
##  [8] "CST7"    "CX3CR1"  "DIAPH2"  "ETNK1"   "GZMM"    "MCTP2"   "NCBP3"  
## [15] "PLEK"    "PPP2R5B" "PTGDR"   "PTPN7"   "RNPEPL1" "TTC16"  
## [1] "found 20 genes."

## [1] 8
##  [1] "AC008105.3"  "AC025171.2"  "ADA2"        "AK5"         "ARRDC2"     
##  [6] "CHRM3-AS2"   "DNASE1"      "GSTM4"       "KLF7"        "NRIP1"      
## [11] "NUAK2"       "PDE7A"       "RNASEH1-AS1" "SLC22A17"    "TUBD1"      
## [16] "TUBE1"       "ZNF84"       "ZNF862"      "SPTLC2"      "TMEM62"     
## [1] "found 16 genes."

## [1] 9
##  [1] "ANKH"     "CSRNP1"   "DHRS3"    "EPHX2"    "KANSL2"   "OXLD1"   
##  [7] "PECAM1"   "ZNF10"    "C12orf75" "GON4L"    "IL4R"     "INPP5D"  
## [13] "KMT2B"    "NARF"     "PHF20"    "PHF20L1"  "SP140"    "TNFRSF4" 
## [1] "found 18 genes."

## [1] 10
##  [1] "MFSD14C"    "STARD7"     "WAPL"       "ABHD3"      "AC016831.7"
##  [6] "AC022916.1" "AC118549.1" "CARMIL2"    "EAPP"       "ECPAS"     
## [11] "KANSL1-AS1" "NRDC"       "PARP11"     "PUM3"       "RAPGEF1"   
## [16] "SLC20A2"    "SPATA13"    "TM2D1"      "UTP25"      "Z93930.2"  
## [1] "found 14 genes."

## [1] 11
##  [1] "BCL3"      "C20orf204" "DDX3Y"     "EIF1AY"    "FAAH2"     "HRH2"     
##  [7] "KDM5D"     "OSM"       "PCSK1N"    "RPS4Y1"    "S100A12"   "SLF2"     
## [13] "SOCS3"     "TTTY15"    "UTY"       "ZFYVE28"  
## [1] "found 15 genes."

## [1] 12
##  [1] "AC145124.1"   "AIF1"         "AKIRIN1"      "BOLA2-SMG1P6" "C12orf45"    
##  [6] "COQ10B"       "CRLF3"        "IL16"         "LINC01550"    "MMP28"       
## [11] "MYNN"         "NUDT4"        "OSER1"        "OTULINL"      "PECR"        
## [16] "TMEM161B-AS1" "TMEM71"       "YY1AP1"       "JAKMIP1"      "SERTAD3"     
## [21] "SUSD6"        "TMEM138"     
## [1] "found 18 genes."

## [1] 13
##  [1] "DELE1"    "DSE"      "GIMAP1"   "IER5"     "KLRB1"    "PITPNC1" 
##  [7] "RAB37"    "SLC25A33" "SNX18"    "TBC1D10C" "TRBC2"    "TTC31"   
## [13] "UCP2"     "APOBEC3G" "GNPTAB"   "GZMB"     "KLRG1"    "LAG3"    
## [19] "MATK"     "SMPD2"   
## [1] "found 20 genes."

## [1] 14
##  [1] "ERCC5"   "FAM8A1"  "BROX"    "CCDC88B" "CD320"   "CISH"    "CTBS"   
##  [8] "FKBP11"  "IL2RB"   "IL2RG"   "KCNAB2"  "PRDM1"   "PREP"    "PVT1"   
## [15] "REXO2"   "RNMT"    "STAT4"   "TGS1"    "TSHZ2"   "UGCG"   
## [1] "found 19 genes."

## [1] 15
##  [1] "AC084033.3" "AMD1"       "CAMK4"      "CCDC141"    "CXorf57"   
##  [6] "EVI2B"      "FAM102A"    "FAM117B"    "FYB1"       "INPP4B"    
## [11] "IPCEF1"     "MAML2"      "MTRNR2L12"  "SNHG12"     "TC2N"      
## [16] "TMC8"       "TMEM107"    "TSC22D2"    "ADAM19"     "SCAMP4"    
## [21] "ZNF292"    
## [1] "found 18 genes."

## [1] 16
##  [1] "ATAD1"    "BTN3A1"   "CHMP1B"   "CHMP7"    "COG5"     "DBP"     
##  [7] "DIP2B"    "LRRC8D"   "NSMAF"    "PARP16"   "PCNP"     "PPP1R15B"
## [13] "SPIDR"    "STX16"    "THAP6"    "TMEM245"  "TSPYL4"   "ZBTB25"  
## [19] "ZMAT1"    "BTN3A2"   "NEK9"     "TAOK3"   
## [1] "found 22 genes."

## [1] 17
##  [1] "AC016405.3" "AC020911.2" "AC025171.3" "AC091271.1" "AC103591.3"
##  [6] "AF213884.3" "AL121944.1" "AL357060.1" "AL451085.1" "C6orf99"   
## [11] "ID3"        "JAML"       "KLF12"      "LINC01465"  "LRRN3"     
## [16] "OSER1-DT"   "PARP8"      "PNISR"      "CNOT4"      "SDF2"      
## [21] "WDR7"      
## [1] "found 9 genes."

## [1] 18
##  [1] "AL627171.1"  "NDUFV2-AS1"  "ZNF490"      "ADTRP"       "ATAD2B"     
##  [6] "CEMIP2"      "CRYBG1"      "GRK2"        "IGLV3-25"    "KIAA0040"   
## [11] "LRRC58"      "MT1X"        "NORAD"       "SLFN12L"     "SNHG9"      
## [16] "TENT5C"      "THUMPD3-AS1" "TRBV6-1"     "UBALD2"      "VPS13D"     
## [1] "found 15 genes."

## [1] 19
##  [1] "CLK4"    "MYADM"   "ZNF821"  "BLOC1S6" "C2orf68" "CD7"     "CLASRP" 
##  [8] "IFNAR1"  "KLF9"    "NME3"    "P4HTM"   "PIK3CB"  "PIM2"    "PRMT2"  
## [15] "RNF145"  "SACS"    "SETD5"   "SLC35A2" "SNX9"    "SP140L" 
## [1] "found 20 genes."

## [1] 20
##  [1] "AC025159.1"  "AL135791.1"  "CERNA1"      "LDLRAP1"     "LINC02273"  
##  [6] "LRRC8C-DT"   "LYRM9"       "NSMCE3"      "PITPNA-AS1"  "SNHG7"      
## [11] "TSPOAP1-AS1" "AC020915.3"  "GPR132"      "HACD3"       "MFSD14A"    
## [16] "NNT-AS1"     "NSD3"        "TOMM70"      "TSPAN14"     "TUT4"       
## [1] "found 10 genes."

## [1] 21
##  [1] "ADK"     "ARL6IP1" "C6orf62" "EFCAB2"  "HEATR5B" "MBD6"    "MTERF4" 
##  [8] "ST3GAL1" "STMN3"   "TOB2"    "TPP2"    "EHMT1"   "FRY"     "FRYL"   
## [15] "ICE1"    "SDR39U1" "SYNRG"   "UBA7"    "UBE3B"   "VPS36"  
## [1] "found 20 genes."

## [1] 22
##  [1] "CBLL1"    "CST3"     "FAM118A"  "FCN1"     "GIMAP8"   "IGKV1-5" 
##  [7] "IGLV1-44" "NT5DC1"   "PYROXD1"  "RABL2B"   "ALOX5AP"  "GAB3"    
## [13] "IFI44"    "KIAA1551" "MX2"      "OAS2"     "PPP2R3C"  "SRP54"   
## [19] "STK10"   
## [1] "found 19 genes."

## [1] 23
##  [1] "RBKS"       "SUPT20H"    "AC116407.2" "APOL6"      "ARHGEF3"   
##  [6] "ATXN7L3B"   "C4orf48"    "CARD16"     "ENY2"       "GIMAP7"    
## [11] "LPIN1"      "LPIN2"      "MESD"       "PDE4B"      "PHPT1"     
## [16] "PTGER2"     "RCBTB2"     "RNF19A"     "TCAF2"      "TMEM156"   
## [1] "found 18 genes."

## [1] 24
##  [1] "AL118516.1" "KIF9"       "RGS10"      "UPF3A"      "BUD23"     
##  [6] "CD69"       "CYTIP"      "DDIT4"      "EFR3A"      "GIMAP4"    
## [11] "IFITM2"     "ISG20"      "KLF6"       "MTRNR2L8"   "NAA38"     
## [16] "NADSYN1"    "NBDY"       "SIGIRR"     "SMIM37"     "STK17B"    
## [1] "found 19 genes."

## [1] 25
##  [1] "CD38"      "IGLV2-14"  "KIAA1328"  "MBNL2"     "RPS26"     "SIMC1"    
##  [7] "XIST"      "APOL1"     "CCL5"      "CCR4"      "GZMA"      "LINC01871"
## [13] "MYO1G"     "RAP1GAP2"  "RSAD2"     "SAMD9L"    "SPON2"     "TGFBR3"   
## [19] "VCAN"     
## [1] "found 17 genes."

## [1] 26
##  [1] "NFYB"    "PHC1"    "ANK3"    "ARID5B"  "CCDC12"  "CREBZF"  "GCN1"   
##  [8] "IL32"    "NFE2L1"  "NQO2"    "NT5C"    "PCGF5"   "PLAC8"   "SYTL1"  
## [15] "TIPARP"  "TMED4"   "XBP1"    "ZDHHC20" "ZNF593" 
## [1] "found 19 genes."

## [1] 27
##  [1] "AC009061.2" "AL645728.1" "AP002360.1" "C12orf29"   "COX10"     
##  [6] "FBXO8"      "GIMAP6"     "HDHD2"      "IL6R"       "KLHL6"     
## [11] "LST1"       "MAST4"      "NBPF14"     "OTUD5"      "RETREG1"   
## [16] "SMDT1"      "TBCK"       "TRAV8-6"    "ZFP14"      "BISPR"     
## [21] "C12orf4"    "PARP4"     
## [1] "found 18 genes."

## [1] 28
##  [1] "CD28"    "KLF10"   "ODC1"    "SH3YL1"  "AGAP2"   "AP3M2"   "AREG"   
##  [8] "CRIP2"   "CRTC3"   "EDA"     "GABPB2"  "ICOS"    "IL21R"   "KHNYN"  
## [15] "LTBP3"   "LY96"    "NFKBIZ"  "PLEKHA2" "SMAD5"   "TOB1"    "ZNF101" 
## [1] "found 21 genes."

## [1] 29
##  [1] "C16orf74"  "C1GALT1"   "COQ8A"     "CTSF"      "FCMR"      "HIVEP2"   
##  [7] "LEPROT"    "LIMD2"     "LIPT1"     "MLXIP"     "ORC4"      "PCMTD2"   
## [13] "RASA2"     "SPART"     "TBC1D7"    "TMEM154"   "TRABD2A"   "TRAV23DV6"
## [19] "ZNF140"    "NDUFC1"    "TMEM175"  
## [1] "found 21 genes."

## [1] 30
##  [1] "DPEP2"   "FAM227B" "GGT7"    "MAP3K8"  "ZFX"     "ASCL2"   "B3GALT4"
##  [8] "CCDC112" "CD58"    "FAM129A" "GALNS"   "IFIT1"   "IFIT2"   "IFIT3"  
## [15] "NBEAL2"  "NRROS"   "PHF23"   "POGLUT1" "ZEB2"    "ZNF276" 
## [1] "found 20 genes."

## [1] 31
##  [1] "RNASEK"   "ARHGAP10" "BCL9L"    "CARD11"   "CMIP"     "CROT"    
##  [7] "DENND4B"  "EIF2AK4"  "GPRIN3"   "IFI35"    "KIF21A"   "KIF21B"  
## [13] "KLHDC4"   "LY6E"     "PLA2G16"  "PRDM2"    "PREX1"    "SBNO2"   
## [19] "SCAF8"    "SLA"     
## [1] "found 20 genes."

## [1] 32
##  [1] "AC004687.1" "AC027644.3" "AC097376.2" "AL359220.1" "CASP4"     
##  [6] "COQ10A"     "GOLGA8B"    "GZMK"       "KCNK6"      "MATR3-1"   
## [11] "MUC20-OT1"  "RGS1"       "TRAV12-2"   "TRAV25"     "TRAV41"    
## [16] "TRBV6-5"    "WASHC4"     "ZNF600"     "ZNF91"      "FRMD4B"    
## [21] "SPOCK2"    
## [1] "found 15 genes."

## [1] 33
##  [1] "ACADSB"   "C3orf58"  "COL18A1"  "DAPP1"    "FAM153C"  "INTS6"   
##  [7] "IP6K2"    "MYLIP"    "NABP1"    "NEK1"     "NR1D1"    "NR1D2"   
## [13] "PLEKHM1"  "RCSD1"    "SLC26A11" "TECPR1"   "DOCK11"   "LPCAT4"  
## [19] "PPRC1"   
## [1] "found 18 genes."

## [1] 34
##  [1] "BTG1"    "BTG2"    "C1orf43" "EGR1"    "FBXL3"   "LCLAT1"  "TCF7"   
##  [8] "ATP8B2"  "CHD6"    "ETV6"    "FBXO9"   "IFNGR2"  "KIF3B"   "NEAT1"  
## [15] "PCED1B"  "PIEZO1"  "RHOH"    "TBC1D14" "ZNF708" 
## [1] "found 18 genes."

## [1] 35
##  [1] "ODF2L"  "UTP6"   "YPEL5"  "ANKAR"  "DTX3L"  "FAM53B" "GBP1"   "GBP3"  
##  [9] "GBP5"   "GNLY"   "HSH2D"  "IFI44L" "IRF1"   "IRF9"   "MX1"    "MYO1F" 
## [17] "NKG7"   "PARP14" "PARP9"  "XAF1"  
## [1] "found 20 genes."

## [1] 36
##  [1] "AC013264.1" "ACSS1"      "AL138963.3" "ANXA2R"     "C7orf31"   
##  [6] "CFAP36"     "LINC00623"  "METAP1"     "METTL21A"   "SNHG8"     
## [11] "SP3"        "STK19"      "TRAV12-1"   "TRAV13-2"   "TRAV21"    
## [16] "TRAV8-3"    "TRAV9-2"    "TRBV28"     "TRBV6-2"    "ZFAS1"     
## [21] "ZNF749"     "C1orf162"  
## [1] "found 17 genes."

## [1] 37
##  [1] "ARHGAP15"  "ATG13"     "CD40LG"    "DPYD"      "ERAP2"     "HOXB2"    
##  [7] "IGKV3-20"  "LAX1"      "SGSM3"     "SLC7A6"    "TCP11L2"   "TGIF1"    
## [13] "TRAV14DV4" "TRBC1"     "TTC39C"    "UBL3"      "XRRA1"     "CARD8-AS1"
## [19] "MT2A"      "OAS1"     
## [1] "found 19 genes."

## [1] 38
##  [1] "AC004854.2" "AC015982.1" "AC023157.3" "AC083880.1" "AC087623.3"
##  [6] "ARF4-AS1"   "BX284668.6" "HIPK1-AS1"  "JCHAIN"     "KCNQ1OT1"  
## [11] "LETM2"      "LINC00649"  "MZF1-AS1"   "NOCT"       "NPIPB11"   
## [16] "NPIPB5"     "PHLDA1"     "SDR42E2"    "THAP9-AS1"  "TOX"       
## [21] "MYBL1"     
## [1] "found 9 genes."

## [1] 39
##  [1] "ABCC10"    "ADGRG1"    "AKNA"      "CCL4"      "CD300A"    "CTSW"     
##  [7] "FCRL6"     "FGFBP2"    "GPR65"     "MIAT"      "PAXX"      "RASAL3"   
## [13] "S1PR5"     "TRANK1"    "TRAV29DV5" "TRBV12-3"  "TSPAN32"   "TTC38"    
## [19] "USP30-AS1" "ZNF683"   
## [1] "found 18 genes."

## [1] 40
##  [1] "ARMH1"    "COA1"     "LRMP"     "RAB33B"   "RNF139"   "TRAV8-2" 
##  [7] "ZSCAN18"  "APH1B"    "CITED4"   "COL6A3"   "COX17"    "HELB"    
## [13] "RNF157"   "RTKN2"    "SESN3"    "SLC23A2"  "SLC25A37" "SLC9A8"  
## [19] "TAF4B"    "ZNF267"  
## [1] "found 20 genes."

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  4156999 222.1   11673970 623.5         NA 11673970 623.5
## Vcells 20567925 157.0   51369168 392.0      65536 51368243 392.0
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5